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COSMIC: exploring the world's knowledge of somatic mutations in human cancer.

Forbes SA, Beare D, Gunasekaran P, Leung K, Bindal N, Boutselakis H, Ding M, Bamford S, Cole C, Ward S, Kok CY, Jia M, De T, Teague JW, Stratton MR, McDermott U, Campbell PJ - Nucleic Acids Res. (2014)

Bottom Line: To emphasize depth of knowledge on known cancer genes, mutation information is curated manually from the scientific literature, allowing very precise definitions of disease types and patient details.In addition, COSMIC also details more than six million noncoding mutations, 10,534 gene fusions, 61,299 genome rearrangements, 695,504 abnormal copy number segments and 60,119,787 abnormal expression variants.All these types of somatic mutation are annotated to both the human genome and each affected coding gene, then correlated across disease and mutation types.

View Article: PubMed Central - PubMed

Affiliation: Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, CB10 1SA. saf@sanger.ac.uk.

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Related in: MedlinePlus

COSMIC website front page. Search options are presented in the left hand panel, descriptions of the content in the right side panel. The lower panel details related websites and other components of COSMIC. The dark bar at the top provides primary navigation to Help, Downloads and other descriptive content as well as a Contact link to the COSMIC helpdesk. Primary access to COSMIC is via the Search box in the left side panel, accepting multiple parameters including gene names, disease descriptions, mutation syntax and stable COSMIC IDs. ‘Search via Cancer Browser’ raises a new page providing navigation of mutation spectra behind thousands of cancer disease classifications.
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Figure 1: COSMIC website front page. Search options are presented in the left hand panel, descriptions of the content in the right side panel. The lower panel details related websites and other components of COSMIC. The dark bar at the top provides primary navigation to Help, Downloads and other descriptive content as well as a Contact link to the COSMIC helpdesk. Primary access to COSMIC is via the Search box in the left side panel, accepting multiple parameters including gene names, disease descriptions, mutation syntax and stable COSMIC IDs. ‘Search via Cancer Browser’ raises a new page providing navigation of mutation spectra behind thousands of cancer disease classifications.

Mentions: The COSMIC website is available at http://cancer.sanger.ac.uk. Designed to make entry to COSMIC easy via one search box, the homepage (Figure 1) also provides access to a number of related resources. Three parallel websites allow the exploration of components of the COSMIC system. ‘COSMIC cell line project’ exclusively displays the results of genomic analysis across a large set of common cancer cell lines, currently numbering 1015 but expected to grow toward 1500. ‘COSMIC whole genomes’ displays only the genome-wide tumor analyses integrated into COSMIC, providing a view across the breadth of cancer genome data without any specific biases introduced via literature curation. ‘COSMIC’ displays all the data brought into the system across the project's life, including cell lines, whole genomes and all genome-wide and gene-specific literature curations. Additionally, ‘COSMIC genome browser’ provides a genomic view across all COSMIC data types, aligned with many annotations from Ensembl, including noncoding RNAs (not yet included in the COSMIC website). ‘Census’ shows a listing of all the genes in the Cancer Gene Census including the details on disease causation and mutation mechanisms. Finally, ‘Drug Sensitivity’ links to a parallel resource in the team, describing the relationship, across more than 700 cell lines, between original disease, mutant genotype and response to a range of anticancer drugs. (9).


COSMIC: exploring the world's knowledge of somatic mutations in human cancer.

Forbes SA, Beare D, Gunasekaran P, Leung K, Bindal N, Boutselakis H, Ding M, Bamford S, Cole C, Ward S, Kok CY, Jia M, De T, Teague JW, Stratton MR, McDermott U, Campbell PJ - Nucleic Acids Res. (2014)

COSMIC website front page. Search options are presented in the left hand panel, descriptions of the content in the right side panel. The lower panel details related websites and other components of COSMIC. The dark bar at the top provides primary navigation to Help, Downloads and other descriptive content as well as a Contact link to the COSMIC helpdesk. Primary access to COSMIC is via the Search box in the left side panel, accepting multiple parameters including gene names, disease descriptions, mutation syntax and stable COSMIC IDs. ‘Search via Cancer Browser’ raises a new page providing navigation of mutation spectra behind thousands of cancer disease classifications.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383913&req=5

Figure 1: COSMIC website front page. Search options are presented in the left hand panel, descriptions of the content in the right side panel. The lower panel details related websites and other components of COSMIC. The dark bar at the top provides primary navigation to Help, Downloads and other descriptive content as well as a Contact link to the COSMIC helpdesk. Primary access to COSMIC is via the Search box in the left side panel, accepting multiple parameters including gene names, disease descriptions, mutation syntax and stable COSMIC IDs. ‘Search via Cancer Browser’ raises a new page providing navigation of mutation spectra behind thousands of cancer disease classifications.
Mentions: The COSMIC website is available at http://cancer.sanger.ac.uk. Designed to make entry to COSMIC easy via one search box, the homepage (Figure 1) also provides access to a number of related resources. Three parallel websites allow the exploration of components of the COSMIC system. ‘COSMIC cell line project’ exclusively displays the results of genomic analysis across a large set of common cancer cell lines, currently numbering 1015 but expected to grow toward 1500. ‘COSMIC whole genomes’ displays only the genome-wide tumor analyses integrated into COSMIC, providing a view across the breadth of cancer genome data without any specific biases introduced via literature curation. ‘COSMIC’ displays all the data brought into the system across the project's life, including cell lines, whole genomes and all genome-wide and gene-specific literature curations. Additionally, ‘COSMIC genome browser’ provides a genomic view across all COSMIC data types, aligned with many annotations from Ensembl, including noncoding RNAs (not yet included in the COSMIC website). ‘Census’ shows a listing of all the genes in the Cancer Gene Census including the details on disease causation and mutation mechanisms. Finally, ‘Drug Sensitivity’ links to a parallel resource in the team, describing the relationship, across more than 700 cell lines, between original disease, mutant genotype and response to a range of anticancer drugs. (9).

Bottom Line: To emphasize depth of knowledge on known cancer genes, mutation information is curated manually from the scientific literature, allowing very precise definitions of disease types and patient details.In addition, COSMIC also details more than six million noncoding mutations, 10,534 gene fusions, 61,299 genome rearrangements, 695,504 abnormal copy number segments and 60,119,787 abnormal expression variants.All these types of somatic mutation are annotated to both the human genome and each affected coding gene, then correlated across disease and mutation types.

View Article: PubMed Central - PubMed

Affiliation: Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, CB10 1SA. saf@sanger.ac.uk.

Show MeSH
Related in: MedlinePlus